Updated LightGBM to 4.1 and Optuna to 3.3, and the other packages #29

EchoDel · 2023-09-28T09:57:02Z

Mainly updated LightGBM to the more recent 4.0 release, although optuna was an easy update as well.
My company expects packages to update to the major version before releasing anything.

I ensured that all the test suite ran before submitting the PR

StatMixedML

Thanks for your PR. Two minor things:

can you please silent the lgb output during cv and training in model.py
can you please use version 4.1.0 in the setup.py

Thanks

EchoDel · 2023-10-02T16:40:01Z

So I've addressed the second comment but I'm not sure its possible to address point 1 for now.

I've dug into the changelog and code and I can't see anyway to suppress the message.
This is the only mention in the changelog and it doesn't even have the commit message.
[python-package] remove 'fobj' in favor of passing custom objective func...

when you look in the parameters its not really mentioned that you can use a custom objective function, although in the python API its mentioned in the notes that you can do that, but nothing about how to suppress the message.

Finally in the source code the message is created when the objective function isn't the base one with no statement for overriding it.
https://github.com/microsoft/LightGBM/blob/63a882b7400a19485727cc808e4715897e63635a/src/c_api.cpp#L322

StatMixedML · 2023-10-02T20:04:16Z

Thanks for your changes. Can you please open an issue on the LightGBM repo asking how to silence the output. Thanks.

EchoDel · 2023-10-03T17:36:21Z

So I've just seen this issue already exists in the lightgbm repo.

microsoft/LightGBM#6014

I'm not sure if you want the temporary work around of the custom logger class implemented?

StatMixedML · 2023-10-04T07:38:31Z

Does the custom logger verbose output for both .cv and .train?

StatMixedML · 2023-10-27T12:30:45Z

@EchoDel To keep the PR open, can you please check the open issues on the verbosity, thanks.

EchoDel · 2023-11-15T14:02:36Z

Sorry for the delay. Yeh this would fix both since we register it with lgbm at the start

StatMixedML · 2023-11-24T09:46:58Z

@EchoDel Using the suggestion from the lightgbm-issue does not work.

I am using

import lightgbm as lgb
class CustomLogger:
    def init(self):
        self.logger = logging.getLogger('lightgbm_custom')
        self.logger.setLevel(logging.ERROR)

    def info(self, message):
        self.logger.info(message)
    
    def warning(self, message):
        # Suppress warnings by not doing anything
        pass
    
    def error(self, message):
        self.logger.error(message)

lgb.register_logger(CustomLogger())

and this gives the following. Can you please look into this.

Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'
Exception ignored on calling ctypes callback function: <function _log_callback at 0x0000026D45999760>
Traceback (most recent call last):
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 205, in _log_callback
    _log_native(str(msg.decode('utf-8')))
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 183, in wrapper
    return func(msg)
           ^^^^^^^^^
  File "C:\Users\maerzale\.virtualenvs\LightGBMLSS-8W0JA8W6\Lib\site-packages\lightgbm\basic.py", line 200, in _log_native
    getattr(_LOGGER, _INFO_METHOD_NAME)(msg)
  File "C:\Users\maerzale\AppData\Local\Temp\ipykernel_14620\1534461007.py", line 7, in info
AttributeError: 'CustomLogger' object has no attribute 'logger'

This suppresses the messages for lightgbm version 4.1

EchoDel · 2023-11-25T16:28:15Z

I think this push has got the custom logger working.

There are alot of other packages which have been updated, particularly torch which had an issues in 2.1.0 and 2.0.1 which I could wrap into this PR is you want.

StatMixedML · 2023-11-28T13:04:20Z

@EchoDel Is the custom logger working now? Haven't tested it yet

EchoDel · 2023-11-28T19:35:22Z

Yep, the logger suppresses all the warning messages

lightgbmlss/model.py

StatMixedML · 2023-11-29T13:46:44Z

I think this push has got the custom logger working.

There are alot of other packages which have been updated, particularly torch which had an issues in 2.1.0 and 2.0.1 which I could wrap into this PR is you want.

Yes please, thanks. The updated packages are

"lightgbm~=4.1.0",
"torch~=2.1.1",
"pyro-ppl~=1.8.6",
"optuna~=3.4.0",
"properscoring~=0.1",
"scikit-learn~=1.3.2",
"numpy~=1.26.2",
"pandas~=2.1.3",
"plotnine~=0.12.4",
"scipy~=1.11.4",
"seaborn~=0.13.0",
"tqdm~=4.66.1",
"matplotlib~=3.8.2",
"ipython~=8.18.1",

StatMixedML · 2023-11-30T10:55:35Z

@EchoDel Thanks for updating the dependencies. Can you please fix the remaining comments so that I can merge the PR. Thanks

…LightGBMLSS into feature/package_updates

EchoDel · 2023-12-05T00:33:01Z

The outstanding requests should be done.

codecov-commenter · 2023-12-06T09:09:09Z

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StatMixedML · 2023-11-29T09:11:01Z

lightgbmlss/model.py

@@ -263,9 +265,9 @@ def cv(self,
        self.set_params(params)
        self.set_init_score(train_set)

+        params['objective'] = self.dist.objective_fn


this is not needed if moved to set_params

StatMixedML · 2023-11-29T13:12:09Z

lightgbmlss/model.py

@@ -389,13 +391,13 @@ def objective(trial):
                                          callbacks=[pruning_callback, early_stopping_callback],
                                          seed=seed,
                                          )
-
+            print(lgblss_param_tuning)


Why do we need it?

Updated LightGBM to 4.1 and Optuna to 3.3 and made the test work

2f326dc

StatMixedML requested changes Sep 29, 2023

View reviewed changes

Aligned the requirement to 4.1.0

cca4364

Added the custom logger to lightgbm

340afab

This suppresses the messages for lightgbm version 4.1

StatMixedML reviewed Nov 29, 2023

View reviewed changes

lightgbmlss/model.py Outdated Show resolved Hide resolved

Updated the other packages

a0e7b91

EchoDel changed the title ~~Updated LightGBM to 4.1 and Optuna to 3.3 and made the test work~~ Updated LightGBM to 4.1 and Optuna to 3.3, and the other packages Nov 29, 2023

EchoDel added 3 commits December 4, 2023 23:32

Moved the objective parameter setting into the main set_params method

b62728d

Merge branch 'feature/package_updates' of https://github.com/EchoDel/…

3b3cff4

…LightGBMLSS into feature/package_updates

removed the other objective in the dict

2fa3eac

StatMixedML approved these changes Dec 6, 2023

View reviewed changes

StatMixedML merged commit 5f31fc2 into StatMixedML:master Dec 6, 2023
3 of 4 checks passed

EchoDel deleted the feature/package_updates branch December 19, 2023 10:51

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Updated LightGBM to 4.1 and Optuna to 3.3, and the other packages #29

Updated LightGBM to 4.1 and Optuna to 3.3, and the other packages #29

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Updated LightGBM to 4.1 and Optuna to 3.3, and the other packages #29

Updated LightGBM to 4.1 and Optuna to 3.3, and the other packages #29

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